I am not aware of any countries with an embargo on running JS.
It's the user's choice to disable JS.
An application shell that acts more like an installable app than a website, using Service Worker and caching data can perform a lot better on worse networks than a classic website.
Yes, that can be combined with server-rendered first load, but that's a ton of added complexity for developers.
Seems strange they go to such an extreme in the exact opposite direction.
What is described here and what I spotted myself seems like something that would benefit Wikipedia and allrecipes.com, but not GitHub of all things.

(And yes, the dark web should use modern web development practices as well, it's essential considering the bandwidth and latency impact)

Ok probably there's some miscommunication here. GitHub has always been a progressive website (not progressive web app, just a website with progressive enhancement), it just was a mish mosh of JS with jQuery, they documented over the years the evolution of the web app and now they decided to remove jQuery. That's it.

As described in the article: they had a website that worked made with jQuery, the goal was to send less JS so they replaced jQuery with native JavaScript and a few polyfills. I think that's all the rationale :-)